data_D1M
#

_chem_comp.id                                   D1M
_chem_comp.name                                 "5-ethynyl-1-(beta-D-glucopyranosyl)pyrimidine-2,4(1H,3H)-dione"
_chem_comp.type                                 D-saccharide
_chem_comp.pdbx_type                            ATOMS
_chem_comp.formula                              "C12 H14 N2 O7"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        
;5-ethynyl-1-(beta-D-glucosyl)pyrimidine-2,4(1H,3H)-dione; 5-ethynyl-1-(D-glucosyl)pyrimidine-2,4(1H,3H)-dione;
5-ethynyl-1-(glucosyl)pyrimidine-2,4(1H,3H)-dione
;

_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2012-04-12
_chem_comp.pdbx_modified_date                   2020-07-17
_chem_comp.pdbx_ambiguous_flag                  N
_chem_comp.pdbx_release_status                  REL
_chem_comp.pdbx_replaced_by                     ?
_chem_comp.pdbx_replaces                        ?
_chem_comp.formula_weight                       298.249
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    D1M
_chem_comp.pdbx_model_coordinates_details       ?
_chem_comp.pdbx_model_coordinates_missing_flag  N
_chem_comp.pdbx_ideal_coordinates_details       Corina
_chem_comp.pdbx_ideal_coordinates_missing_flag  N
_chem_comp.pdbx_model_coordinates_db_code       4EL5
_chem_comp.pdbx_subcomponent_list               ?
_chem_comp.pdbx_processing_site                 RCSB
#   #
loop_
_pdbx_chem_comp_synonyms.ordinal
_pdbx_chem_comp_synonyms.comp_id
_pdbx_chem_comp_synonyms.name
_pdbx_chem_comp_synonyms.provenance
_pdbx_chem_comp_synonyms.type
1  D1M  "5-ethynyl-1-(beta-D-glucosyl)pyrimidine-2,4(1H,3H)-dione"  PDB  ?  
2  D1M  "5-ethynyl-1-(D-glucosyl)pyrimidine-2,4(1H,3H)-dione"       PDB  ?  
3  D1M  "5-ethynyl-1-(glucosyl)pyrimidine-2,4(1H,3H)-dione"         PDB  ?  
#   #
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.alt_atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.charge
_chem_comp_atom.pdbx_align
_chem_comp_atom.pdbx_aromatic_flag
_chem_comp_atom.pdbx_leaving_atom_flag
_chem_comp_atom.pdbx_stereo_config
_chem_comp_atom.model_Cartn_x
_chem_comp_atom.model_Cartn_y
_chem_comp_atom.model_Cartn_z
_chem_comp_atom.pdbx_model_Cartn_x_ideal
_chem_comp_atom.pdbx_model_Cartn_y_ideal
_chem_comp_atom.pdbx_model_Cartn_z_ideal
_chem_comp_atom.pdbx_component_atom_id
_chem_comp_atom.pdbx_component_comp_id
_chem_comp_atom.pdbx_ordinal
D1M  N1   N1      N  0  1  N  N  N  34.097  23.508  28.807   0.974   0.008  -0.068  N1   D1M   1  
D1M  C2A  C2      C  0  1  N  N  N  33.494  24.363  29.765   1.230   0.222   1.232  C2A  D1M   2  
D1M  O2A  O2      O  0  1  N  N  N  32.281  24.570  29.788   0.300   0.295   2.013  O2A  D1M   3  
D1M  N3   N3      N  0  1  N  N  N  34.319  25.037  30.686   2.484   0.357   1.697  N3   D1M   4  
D1M  C4A  C4      C  0  1  N  N  N  35.673  24.807  30.700   3.535   0.281   0.854  C4A  D1M   5  
D1M  O4A  O4      O  0  1  N  N  N  36.304  25.448  31.522   4.674   0.402   1.268  O4A  D1M   6  
D1M  C5A  C5      C  0  1  N  N  N  36.293  23.901  29.807   3.277   0.047  -0.575  C5A  D1M   7  
D1M  C6A  C6      C  0  1  N  N  N  35.509  23.279  28.838   1.981  -0.083  -0.985  C6A  D1M   8  
D1M  C7   C7      C  0  1  N  N  N  37.709  23.693  29.916   4.357  -0.043  -1.511  C7   D1M   9  
D1M  C8   C8      C  0  1  N  N  N  38.877  23.561  30.059   5.242  -0.116  -2.279  C8   D1M  10  
D1M  C1   "C1'"   C  0  1  N  N  R  33.213  22.851  27.851  -0.414  -0.138  -0.512  C1   D1M  11  
D1M  C2   "C2'"   C  0  1  N  N  R  33.698  23.181  26.343  -1.017  -1.403   0.106  C2   D1M  12  
D1M  O2   "O2'"   O  0  1  N  N  N  33.876  24.575  26.155  -0.299  -2.549  -0.355  O2   D1M  13  
D1M  C3   "C3'"   C  0  1  N  N  S  32.653  22.576  25.422  -2.486  -1.516  -0.313  C3   D1M  14  
D1M  O3   "O3'"   O  0  1  N  N  N  33.097  22.646  24.054  -3.077  -2.653   0.318  O3   D1M  15  
D1M  C4   "C4'"   C  0  1  N  N  S  32.464  21.092  25.856  -3.228  -0.247   0.118  C4   D1M  16  
D1M  O4   "O4'"   O  0  1  N  N  N  31.333  20.596  25.159  -4.583  -0.310  -0.332  O4   D1M  17  
D1M  C5   "C5'"   C  0  1  N  N  R  32.231  20.862  27.418  -2.540   0.973  -0.500  C5   D1M  18  
D1M  O5   "O5'"   O  0  1  N  N  N  33.281  21.431  28.141  -1.170   1.001  -0.095  O5   D1M  19  
D1M  C6   "C6'"   C  0  1  N  N  N  32.109  19.283  27.746  -3.239   2.248  -0.026  C6   D1M  20  
D1M  O6   "O6'"   O  0  1  N  N  N  33.319  18.699  27.236  -2.672   3.378  -0.692  O6   D1M  21  
D1M  HN3  HN3     H  0  1  N  N  N  33.917  25.686  31.332   2.635   0.512   2.643  HN3  D1M  22  
D1M  H6   H6      H  0  1  N  N  N  35.967  22.625  28.111   1.755  -0.256  -2.027  H6   D1M  23  
D1M  H8   H8      H  0  1  N  N  N  39.923  23.443  30.187   6.034  -0.182  -2.965  H8   D1M  24  
D1M  H1   "H1'"   H  0  1  N  N  N  32.183  23.218  27.969  -0.443  -0.216  -1.598  H1   D1M  25  
D1M  H2   "H2'"   H  0  1  N  N  N  34.651  22.656  26.183  -0.951  -1.344   1.193  H2   D1M  26  
D1M  HO2  "HO2'"  H  0  1  N  Y  N  34.160  24.741  25.264  -0.628  -3.387  -0.002  HO2  D1M  27  
D1M  H3   "H3'"   H  0  1  N  N  N  31.700  23.110  25.548  -2.549  -1.626  -1.396  H3   D1M  28  
D1M  HO3  "HO3'"  H  0  1  N  Y  N  32.437  22.265  23.487  -4.009  -2.786   0.097  HO3  D1M  29  
D1M  H4   "H4'"   H  0  1  N  N  N  33.364  20.531  25.564  -3.209  -0.165   1.205  H4   D1M  30  
D1M  HO4  "HO4'"  H  0  1  N  Y  N  31.185  19.689  25.399  -5.079  -1.063   0.018  HO4  D1M  31  
D1M  H5   "H5'"   H  0  1  N  N  N  31.275  21.334  27.690  -2.596   0.910  -1.587  H5   D1M  32  
D1M  H61  "H6'"   H  0  1  N  N  N  32.029  19.119  28.831  -4.302   2.187  -0.256  H61  D1M  33  
D1M  H62  "H6'A"  H  0  1  N  N  N  31.231  18.851  27.244  -3.105   2.357   1.051  H62  D1M  34  
D1M  HO6  "HO6'"  H  0  1  N  Y  N  33.312  17.763  27.398  -3.068   4.223  -0.440  HO6  D1M  35  
#   #
loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.value_order
_chem_comp_bond.pdbx_aromatic_flag
_chem_comp_bond.pdbx_stereo_config
_chem_comp_bond.pdbx_ordinal
D1M  N1   C2A  SING  N  N   1  
D1M  N1   C6A  SING  N  N   2  
D1M  N1   C1   SING  N  N   3  
D1M  C2A  O2A  DOUB  N  N   4  
D1M  C2A  N3   SING  N  N   5  
D1M  N3   C4A  SING  N  N   6  
D1M  C4A  O4A  DOUB  N  N   7  
D1M  C4A  C5A  SING  N  N   8  
D1M  C5A  C6A  DOUB  N  N   9  
D1M  C5A  C7   SING  N  N  10  
D1M  C7   C8   TRIP  N  N  11  
D1M  C1   C2   SING  N  N  12  
D1M  C1   O5   SING  N  N  13  
D1M  C2   O2   SING  N  N  14  
D1M  C2   C3   SING  N  N  15  
D1M  C3   O3   SING  N  N  16  
D1M  C3   C4   SING  N  N  17  
D1M  C4   O4   SING  N  N  18  
D1M  C4   C5   SING  N  N  19  
D1M  C5   O5   SING  N  N  20  
D1M  C5   C6   SING  N  N  21  
D1M  C6   O6   SING  N  N  22  
D1M  N3   HN3  SING  N  N  23  
D1M  C6A  H6   SING  N  N  24  
D1M  C8   H8   SING  N  N  25  
D1M  C1   H1   SING  N  N  26  
D1M  C2   H2   SING  N  N  27  
D1M  O2   HO2  SING  N  N  28  
D1M  C3   H3   SING  N  N  29  
D1M  O3   HO3  SING  N  N  30  
D1M  C4   H4   SING  N  N  31  
D1M  O4   HO4  SING  N  N  32  
D1M  C5   H5   SING  N  N  33  
D1M  C6   H61  SING  N  N  34  
D1M  C6   H62  SING  N  N  35  
D1M  O6   HO6  SING  N  N  36  
#   #
loop_
_pdbx_chem_comp_descriptor.comp_id
_pdbx_chem_comp_descriptor.type
_pdbx_chem_comp_descriptor.program
_pdbx_chem_comp_descriptor.program_version
_pdbx_chem_comp_descriptor.descriptor
D1M  SMILES            ACDLabs               12.01  "O=C1NC(=O)N(C=C1C#C)C2OC(C(O)C(O)C2O)CO"  
D1M  InChI             InChI                 1.03   "InChI=1S/C12H14N2O7/c1-2-5-3-14(12(20)13-10(5)19)11-9(18)8(17)7(16)6(4-15)21-11/h1,3,6-9,11,15-18H,4H2,(H,13,19,20)/t6-,7-,8+,9-,11-/m1/s1"  
D1M  InChIKey          InChI                 1.03   DSYJZEAWLKMMLW-ZBGLXGBJSA-N  
D1M  SMILES_CANONICAL  CACTVS                3.370  "OC[C@H]1O[C@H]([C@H](O)[C@@H](O)[C@@H]1O)N2C=C(C#C)C(=O)NC2=O"  
D1M  SMILES            CACTVS                3.370  "OC[CH]1O[CH]([CH](O)[CH](O)[CH]1O)N2C=C(C#C)C(=O)NC2=O"  
D1M  SMILES_CANONICAL  "OpenEye OEToolkits"  1.7.6  "C#CC1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@H]([C@@H]([C@H](O2)CO)O)O)O"  
D1M  SMILES            "OpenEye OEToolkits"  1.7.6  "C#CC1=CN(C(=O)NC1=O)C2C(C(C(C(O2)CO)O)O)O"  
#   #
loop_
_pdbx_chem_comp_identifier.comp_id
_pdbx_chem_comp_identifier.type
_pdbx_chem_comp_identifier.program
_pdbx_chem_comp_identifier.program_version
_pdbx_chem_comp_identifier.identifier
D1M  "SYSTEMATIC NAME"  ACDLabs               12.01  "5-ethynyl-1-(beta-D-glucopyranosyl)pyrimidine-2,4(1H,3H)-dione"  
D1M  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  1.7.6  "5-ethynyl-1-[(2R,3R,4S,5S,6R)-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]pyrimidine-2,4-dione"  
#   #
loop_
_pdbx_chem_comp_feature.comp_id
_pdbx_chem_comp_feature.type
_pdbx_chem_comp_feature.value
_pdbx_chem_comp_feature.source
_pdbx_chem_comp_feature.support
D1M  "CARBOHYDRATE ISOMER"                  D         PDB  ?  
D1M  "CARBOHYDRATE RING"                    pyranose  PDB  ?  
D1M  "CARBOHYDRATE ANOMER"                  beta      PDB  ?  
D1M  "CARBOHYDRATE PRIMARY CARBONYL GROUP"  aldose    PDB  ?  
#   #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
D1M  "Create component"          2012-04-12  RCSB  
D1M  "Other modification"        2020-07-03  RCSB  
D1M  "Modify synonyms"           2020-07-17  RCSB  
D1M  "Modify internal type"      2020-07-17  RCSB  
D1M  "Modify linking type"       2020-07-17  RCSB  
D1M  "Modify atom id"            2020-07-17  RCSB  
D1M  "Modify component atom id"  2020-07-17  RCSB  
D1M  "Modify leaving atom flag"  2020-07-17  RCSB  
##
